[EMBOSS] sreformat: problems with parameter

[Ulrike Kaule]

Hello,

I want to develop a workflow in Taverna, which accepts a sequence in 
fasta-format and does some analysis with it. But a demand is also, that 
the user could input some other formats than fasta - so I have to 
convert them internally to fasta. The only programm I found for this 
purpose was sreformat from HMMER. At the moment this programm is not 
included in EMBOSS, so I wrote a new acd-file and deployed it as a 
web-service.
The acd-file is as follows:

-----------------------------------------------------
application: sreformat [
  documentation: "Converts sequence file to different format"
  groups: "Utils"
]

section: input [
  information: "Input section"
  type: "page"
]

string: format  [
  parameter: "Y"
  information: "Output format"
]

sequence: seqfile  [
  parameter: "Y"
  information: "Input sequence"
]

endsection: input

section: output [
  information: "Output section"
  type: "page"
]

seqout: outfile  [
  parameter: "Y"
]

endsection: output
-----------------------------------------------------


To ensure, that the output-format of sreformat is 'fasta', I coded it 
hard in a string-constant and gave it to parameter 'osformat' of sreformat.
But the error-message I got was:

----------------------------------------------------------------------------------------
Task failed due to problem invoking soaplab service
    SoaplabTask.execute(..) : line 201 <SoaplabTask.java>
    ProcessorTask.runAndGenerateTemplates(..) : line 444 
<ProcessorTask.java>
    ProcessorTask.doInvocationWithRetryLogic(..) : line 397 
<ProcessorTask.java>
    ProcessorTask.invokeOnce(..) : line 319 <ProcessorTask.java>   
    ProcessorTask.invokeWithoutIteration(..) : line 503<ProcessorTask.java>
    ProcessorTask.invoke(..) : line 251 <ProcessorTask.java>   
    ProcessorTask.handleRun(..) : line 199 <ProcessorTask.java>   
    NewState$1.run(..) : line 67 <NewState.java>
    
    org.embl.ebi.SoaplabShare.SoaplabException: CONFLICTING_INPUT. 
format * (Parameter (Output format): Cannot remain empty.)
    
    SOAPFaultBuilder.createFault(..) : line 221 <SOAPFaultBuilder.java>
    SOAPFaultBuilder.endElement(..) : line 128 <SOAPFaultBuilder.java>
    DeserializationContext.endElement(..) : line 1087 
<DeserializationContext.java>
    AbstractSAXParser.endElement(..) : line -1 <Unknown filename>
    XMLNSDocumentScannerImpl.scanEndElement(..) : line -1 <Unknown filename>
   
 XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(..) : 
line -1 <Unknown filename>
    XMLDocumentFragmentScannerImpl.scanDocument(..) : line -1 <Unknown 
filename>
    XML11Configuration.parse(..) : line -1 <Unknown filename>
    XML11Configuration.parse(..) : line -1 <Unknown filename>
    XMLParser.parse(..) : line -1 <Unknown filename>
    AbstractSAXParser.parse(..) : line -1 <Unknown filename>
    SAXParser.parse(..) : line 345 <SAXParser.java>
    DeserializationContext.parse(..) : line 227 
<DeserializationContext.java>
    SOAPPart.getAsSOAPEnvelope(..) : line 696 <SOAPPart.java>
    Message.getSOAPEnvelope(..) : line 424 <Message.java>
    MustUnderstandChecker.invoke(..) : line 62 <MustUnderstandChecker.java>
    AxisClient.invoke(..) : line 206 <AxisClient.java>
    Call.invokeEngine(..) : line 2754 <Call.java>
    Call.invoke(..) : line 2737 <Call.java&>
    Call.invoke(..) : line 2413 <Call.java>
    Call.invoke(..) : line 2336 <Call.java>
    Call.invoke(..) : line 1793 <Call.java>
    SoaplabTask.execute(..) : line 98 <SoaplabTask.java>
    ProcessorTask.runAndGenerateTemplates(..) : line 444 
<ProcessorTask.java>
    ProcessorTask.doInvocationWithRetryLogic(..) : line 397 
<ProcessorTask.java>
    ProcessorTask.invokeOnce(..) : line 319 <ProcessorTask.java>
    ProcessorTask.invokeWithoutIteration(..) : line 503 <ProcessorTask.java>
    ProcessorTask.invoke(..) : line 251 <ProcessorTask.java>
    ProcessorTask.handleRun(..) : line 199 <ProcessorTask.java>
    NewState$1.run(..) : line 67 <NewState.java>
----------------------------------------------------------------------------------------
So it seems, that the string-constant is not recognized. Therefore I 
changed in the acd-file, the default-value for format to "fasta" :
...
string: format  [
  parameter: "Y"
  information: "Output format"
  default: "fasta"
  standard: "N"
]
...
but I got an error-message too.

Soaplab call returned an error : Summary:
    Completed: Erroneously
    Termination status: 256
    Platform: Linux linux 2.6.4-52-default #1 Wed Apr 7 02:08:30 UTC 
2004 i686 i686 i386 GNU/Linux
    Started: 20.09.2005 20:22:43 (Europe/Berlin)
    Ended: 20.09.2005 20:22:43 (Europe/Berlin)
Report:
Name: sreformat
Started: 05-09-20 20:22:43
Program and parameters:
sreformat
/usr/local/analysis-interfaces/a/unknown/Projects/default/Data/in1127240561172
/usr/local/analysis-interfaces/a/unknown/Projects/default/Data/out1127240561314
--- end of parameters

Completed: 05-09-20 20:22:43

Exit: 1


FATAL: Unknown output format 
/usr/local/analysis-interfaces/a/unknown/Projects/default/Data/in1127240561172
Usage: sreformat [-options] <format> <seqfile>
  Output format choices: Unaligned      Aligned
                         -----------    -------
                         fasta          stockholm
                         embl           msf
                         genbank        a2m
                         gcg            phylip
                         gcgdata        clustal
                         pir            selex
                         raw            eps

  Available options are:
    -h : help; print brief help on version and usage
    -d : force DNA alphabet for nucleic acid sequence
    -r : force RNA alphabet for nucleic acid sequence
    -l : force lower case
    -u : force upper case
    -x : convert non-IUPAC chars in DNA to N's for IUPAC/BLAST compatibility


SoaplabTask.execute(..) : line 151 <SoaplabTask.java>
   ProcessorTask.runAndGenerateTemplates(..) : line 444 <ProcessorTask.java>
   ProcessorTask.doInvocationWithRetryLogic(..) : line 397 
<ProcessorTask.java>
   ProcessorTask.invokeOnce(..) : line 319 <ProcessorTask.java>
   ProcessorTask.invokeWithoutIteration(..) : line 503 <ProcessorTask.java>
   ProcessorTask.invoke(..) : line 251 <ProcessorTask.java>
   ProcessorTask.handleRun(..) : line 199 <ProcessorTask.java>
   NewState$1.run(..) : line 67 <NewState.java>
-----------------------------------------------------------------------------------
My questions are:
1) Is there another programm in emboos, what does the same like 
sreformat - until now I couldn't found some.
2) Is the error-message due to a problem in acd-file or is it a problem 
in soaplab? (At the moment the acd-file is in soaplab-directory 
(analysis-interfaces/metadata/))
3) Is there another way to tell sreformat in acd-file, that the 
output-format should be 'fasta ?

Thank you in advance

Ulrike Kaule